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rfc:rfc4708

Network Working Group A. Miller Request for Comment: 4708 The University of Auckland Category: Informational October 2006

                         CellML Media Type

Status of This Memo

 This memo provides information for the Internet community.  It does
 not specify an Internet standard of any kind.  Distribution of this
 memo is unlimited.

Copyright Notice

 Copyright (C) The Internet Society (2006).

Abstract

 This document standardises a new media type -- application/cellml+xml
 -- for use in exchanging mathematical models represented in a CellML
 Umbrella 1.0 compliant markup language.

1. Introduction

 The CellML Umbrella format is a standardised markup meta-language for
 the interchange of mathematical models.  The CellML Umbrella format
 provides a common base that is supported by a number of specific
 formats used in the interchange of mathematical models.  The CellML
 Umbrella format provides enough information to determine which
 specific language is used to express the model.  The syntax and
 semantics of the CellML Umbrella format are defined by
 [CELLML-UMBRELLA].
 The CellML Umbrella format is an actual media format.  Although
 CellML Umbrella documents contain elements in namespaces defined by
 other specifications such as [RDF] and [MATHML], the elements in
 these namespaces do not contain sufficient information to define a
 mathematical model, and so CellML provides the information required
 to interconnect the different CellML components, as well as the
 information required to link CellML components to their metadata.  As
 such, CellML Umbrella documents are more than just a collection of
 entities defined elsewhere, and so a new media type is required to
 identify CellML.
 As all well-formed CellML Umbrella documents are also well-formed XML
 documents, the convention described in Section 7 of [RFC3023] has
 been observed by use of the +xml suffix.

Miller Informational [Page 1] RFC 4708 CellML Media Type October 2006

 The information in CellML Umbrella documents cannot be interpreted
 without understanding the semantics of the XML elements used to mark
 up the model structure.  Therefore, the application top-level type is
 used instead of the text top-level type.

2. Notational Conventions

 The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT",
 "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this
 document are to be interpreted as described in [RFC2119].
 The terms "element" and "document element" in this document are to be
 interpreted as in [XML].
 The term "XML namespace" is to be interpreted as in [NAMESPACES].

3. Media Type Registration for CellML Umbrella

 MIME media type name: application
 MIME subtype name: cellml+xml
 Mandatory parameters: none
 Optional parameters: charset
    The charset parameter of application/cellml+xml is handled in the
    same fashion as for application/xml, as specified in Section 3.2
    of [RFC3023].  However, per conformance rule 4 of
    [CELLML-UMBRELLA], valid CellML Umbrella documents MUST be in the
    UTF-8 character set.  If the charset parameter is present, it MUST
    take the value "utf-8".  CellML processing software SHOULD check
    the charset field, and if it is present but not equal to "utf-8",
    MAY attempt to recover from the error by processing the document
    in the specified character set.
 Encoding considerations: As per Section 3.2 of [RFC3023].
 Security considerations: As per Section 5 of this document.
 Interoperability considerations: As per Section 4.1 of this document.
 Published specification:
    CellML Umbrella Specification [CELLML-UMBRELLA].
 Applications that use this media type: As per Section 4.2 of this
    document.

Miller Informational [Page 2] RFC 4708 CellML Media Type October 2006

 Additional information:
    Magic number(s): None.
       XML processing software can identify CellML Umbrella documents
       as XML documents that contain a document element with the local
       name "model".
    File extension(s):
       The RECOMMENDED file extension for CellML Umbrella documents is
       .cellml
       Some older software uses the file extension .xml.  Software
       vendors have also used the non-standard extension .cml.  In
       contexts where the MIME type is available, or where the type
       has already been determined as CellML, implementations SHOULD
       allow files to be opened regardless of the extension.
       Implementations transferring models to an environment that uses
       file extensions SHOULD use the .cellml extension.
    Macintosh File Type Code(s): "TEXT"
    Person & email address to contact for further information:
       See the Author's Address section of this document.
    Intended usage: COMMON
    Author/Change controller: The CellML Umbrella 1.0 specification
       was authored by Andrew Miller.
       The CellML Umbrella 1.0 specification itself will not change.
       However, the umbrella specification defines the process for new
       specific formats to be registered.  The Bioengineering
       Institute at The University of Auckland, with input from the
       CellML Community via the cellml-discussion@cellml.org mailing
       list, has control over the CellML Umbrella Format Registry.

4. Interoperability and Usage

4.1. Interoperability Considerations

 The interoperability considerations in Section 3.1 of [RFC3023] also
 apply to CellML Umbrella documents.  CellML Umbrella documents
 contain XML elements defined by each specific format, all of which
 are published specifications.  In addition to the ability to parse
 XML, user agents require software support for the semantics of [RDF]
 and/or part or all of a specific format.  As efforts are made to keep

Miller Informational [Page 3] RFC 4708 CellML Media Type October 2006

 the number of specific formats small, user agents SHOULD implement
 all specific formats listed in the CellML Umbrella Format Registry at
 the time they were developed.

4.2. Applications that Use CellML Umbrella Format

 CellML Umbrella is device-, platform-, and vendor-neutral and is
 supported by a wide range of CellML processing tools, including those
 designed to validate, edit, and/or visualise CellML models, extract
 MathML or RDF, translate to or from other related specifications,
 evaluate mathematics and ordinary differential equations, fit
 parameters to models, and serve, archive, and annotate models.

5. Security Considerations

 As CellML Umbrella is an XML-based markup language, all the security
 considerations presented in Section 10 of [RFC3023] also apply to
 CellML Umbrella.
 Some types of CellML Umbrella documents can refer to other Uniform
 Resource Locators (URLs) in a number of places:
    i)   References to XML document type definitions or schemas.
    ii)  References to other models using the import features of some
         specific formats.
    iii) References to other documents embedded in user-defined data.
 Some types of CellML processing software may then automatically
 attempt to access the URL and retrieve the document.  This retrieval
 could have several consequences, specifically,
    i)   if a CellML document is transferred via e-mail, the fact that
         the recipient has opened the CellML document could be
         disclosed to the sender without the recipient's knowledge or
         consent.
    ii)  where the recipient of a document transfers the document to
         another location using the MIME type defined in this
         document, the original author of the document may be notified
         of the second address by the attempted retrieval of further
         documents.
    iii) by performing requests on the recipient's behalf, the CellML
         processing software may cause actions to be performed with
         privileges granted to the recipient, without the recipient's
         knowledge or consent.

Miller Informational [Page 4] RFC 4708 CellML Media Type October 2006

 CellML processing software can mitigate this threat when running in
 an environment where it is a concern by requiring explicit
 confirmation from the user before attempting to load any external
 documents.

6. IANA Considerations

 This document specifies a new media type.  IANA has added this media
 type to their media types registry as specified in [RFC4288].

7. References

7.1. Normative References

 [CELLML-UMBRELLA] Miller, A.K., "CellML Umbrella Specification 1.0",
                   20 April 2006, <http://www.cellml.org/
                   specifications/cellml_umbrella_1.0>
 [NAMESPACES]      Bray, T., et. al., "Namespaces in XML 1.1", 4
                   February 2004, <http://www.w3.org/TR/xml-names11>
 [RFC2119]         Bradner, S., "Key words for use in RFCs to Indicate
                   Requirement Levels", BCP 14, RFC 2119, March 1997.
 [RFC3023]         Murata, M., St. Laurent, S., and D. Kohn, "XML
                   Media Types", RFC 3023, January 2001.
 [XML]             Bray, T., et. al., "Extensible Markup Language
                   (XML) 1.0 (Fourth Edition)", 29 September 2006,
                   <http://www.w3.org/TR/REC-xml/>

7.2. Informative References

 [MATHML]          Ion, P. and Miner, R.(editors) "Mathematical Markup
                   Language (MathML) 1.01 Specification", 7 July 1999,
                   <http://www.w3.org/TR/REC-MathML/>
 [RDF]             Beckett, D.(editor) "RDF/XML Syntax Specification
                   (Revised)", 10 February 2004,
                   <http://www.w3.org/TR/rdf-syntax-grammar/>
 [RFC4288]         Freed, N. and J. Klensin, "Media Type
                   Specifications and Registration Procedures", BCP
                   13, RFC 4288, December 2005.

Miller Informational [Page 5] RFC 4708 CellML Media Type October 2006

Author's Address

 Andrew Miller
 The Bioengineering Institute at The University of Auckland
 Level 6, 70 Symonds St
 Auckland Central
 Auckland
 EMail: ak.miller@auckland.ac.nz

Miller Informational [Page 6] RFC 4708 CellML Media Type October 2006

Full Copyright Statement

 Copyright (C) The Internet Society (2006).
 This document is subject to the rights, licenses and restrictions
 contained in BCP 78, and except as set forth therein, the authors
 retain all their rights.
 This document and the information contained herein are provided on an
 "AS IS" basis and THE CONTRIBUTOR, THE ORGANIZATION HE/SHE REPRESENTS
 OR IS SPONSORED BY (IF ANY), THE INTERNET SOCIETY AND THE INTERNET
 ENGINEERING TASK FORCE DISCLAIM ALL WARRANTIES, EXPRESS OR IMPLIED,
 INCLUDING BUT NOT LIMITED TO ANY WARRANTY THAT THE USE OF THE
 INFORMATION HEREIN WILL NOT INFRINGE ANY RIGHTS OR ANY IMPLIED
 WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

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 Intellectual Property Rights or other rights that might be claimed to
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Acknowledgement

 Funding for the RFC Editor function is provided by the IETF
 Administrative Support Activity (IASA).

Miller Informational [Page 7]

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